\documentclass[nols]{tufte-book}% or tufte-handout
\hypersetup{colorlinks}% uncomment this line if you prefer colored hyperlinks (e.g., for onscreen viewing)

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% Book metadata
\title{{M}arti{T}racks Manual\thanks{Thanks to Marti, gone but never forgotten.}}
\author[Daniel Rafael Miranda-Esquivel \& Susy Echeverr\'ia]{Daniel Rafael Miranda-Esquivel \& Susy Echeverr\'ia}
%\footnote{20072010}
\usepackage{natbib}
\usepackage{drme}
\usepackage{glossaries}


\bibliographystyle{./diver_distri}

\publisher{Published by the authors}



\input{preamble-tufte.tex}


% Generates the index
\usepackage{makeidx}

\makeindex
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% Front matter
\frontmatter

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% r.3 full title page
\maketitle


% v.4 copyright page
\input{copyleft.tex}

\vfill
\openepigraph{Life and Earth have evolved together}{Leon Croizat}
\openepigraph{Analyses and Software have to evolve together}{The authors}

% r.5 contents
\tableofcontents

\listoffigures

\listoftables

% r.7 dedication
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\nohyphenation
Dedicated to those who appreciate good Biogeography and love dogs.
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\chapter{Forewords}

\input{forewords.tex}

\mainmatter

% r.9 introduction
%\cleardoublepage

\chapter{Introduction}
\label{ch:panbio}

\input{intro.tex}
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% Start the main matter (normal chapters)





\chapter{PanTrack, the program}

\input{pgtrack.tex}



\chapter{Worked examples}

\input{example1.tex}



 

\chapter{PanTrack commands}
\label{ch:commands}
\index{commands}

\section{Text interface mode}
\label{ch:TUI_commands}
\index{commands:text interface}


	general
	
	l == list			List all tracks
	
	
	comparisons *tracks*
		
	a == all			Track all the species using MSTs to compare			
	
	g == group			Track a group of contiguous species
	
	p == pair			Track a pair of species (contiguous or not)
	  
	In all the three cases a new MST=track will be created if the
	species compared are congruent, while in a [p]air comparison
	only a single track could be created. In an [a]ll/[g]roup 
	comparison, there could be more than one track.


	comparisons *segments*
		
	s == all			Track all the species using segments to compare			
		
	t == pair			Track a pair of species (contiguous or not)
	  



	join
	
	u == join group		Join a group of contiguous tracks if a given pair 
						has a minimal congruence equal or higher than the
						minimal congruence inputed in the value file or
						the default value (0.85). If you want to join
						a group regardless of the minimal congruence value,
						reduce the min. cong. value to 0.0. After this late
						analysis, replace the original min. cong. value
						
	j == join pair		Join two, contiguous or not, tracks independent of
						the minimal congruence value
						

	congruence calculation
	
	o == congr. group	Calculate the congruence by pairs of a contiguous group,
						as ther output is a list, is easier to reade a small 
						group than a large group
							
	n == congr. pair	Calculate the congruence of a single pair 
	

	modify decision rules
	
	c == cut			Change the minimal cut value
	r == rules			Modify R1, R2, and R3
	m == min. cong.		Change the minimal congruence value (see join)
	


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% The back matter contains appendices, bibliographies, indices, glossaries, etc.







\backmatter

\bibliography{manual}


\printindex

\end{document}

